Deleting occluded faces
You could write a shader in your engine that gets rid of unwanted faces. The best practice though - depending on the game style - might be to redo the model and make each bodypart piecewise - which is typically what games like half life, n64 and psx titles have done
meaning you start off with one mesh like a head - and then once its where you want it to be in edit mode - you add another mesh for, say a jacket IN EDIT MODE SO ITS ALL PART OF THE SAME MESH GROUP
Its a strange concept at first if you're used to having everything in one mesh but its actually what many games used to do and to top it all off, since youre working with simple geometry rigging and texturing will be super easy
I get what you're saying though. Unfortunantly if you dont want to write a shader you will have to manually delete, shape, and reunwrap your model as fit. It sucks and I understand the pain. Ive done it before myself.